source/pymol/UNRESInpGen.py

   1 # -*- coding: utf-8 -*-
   2 '''
   3 -------------------------------------------------------------------------------
   4  UNRESInpGen.py - UNRES graphical input generator v 1.0
   5 -------------------------------------------------------------------------------
   6
   7  Written by Dawid Jagieła (lightnir@chem.univ.gda.pl)  Oct 2012
   8
   9 '''
  10
  11 from pymol import cmd,stored
  12 from Tkinter import *
  13 import tkFileDialog
  14 import tkMessageBox
  15 import Pmw
  16 import string
  17 import os
  18
  19 UNRESInpGen_version="1.0"
  20
  21 def __init__(self):
  22         self.UNRESInpGenWindow = None
  23         try:
  24                 self.menuBar.addcascademenu('Plugin', 'UNRESPlugins', 'UNRESPACK Plugins', label='UNRES Plugins')
  25         except:
  26                 pass
  27
  28         self.menuBar.addmenuitem('UNRESPlugins', 'command','UNRESInpGen',
  29                 label='UNRES Input Generator',
  30                 command = lambda s=self: createUNRESInpGen(s) )
  31
  32 def createUNRESInpGen(app):
  33         if (app.UNRESInpGenWindow == None):
  34                 app.UNRESInpGenWindow = UNRESInpGenerator(app)
  35         else:
  36                 app.UNRESInpGenWindow.myToggle()
  37
  38 #=================================================================
  39
  40
  41 class UNRESInpGenerator(Toplevel):
  42         global UNRESInpGen_version
  43         # Class variables
  44         """
  45         cv = IntVar()
  46         pp = IntVar()
  47         cp = IntVar()
  48         rv = IntVar()
  49         colorize = IntVar()
  50         """
  51         seq_letter = IntVar()
  52         writeSSbrige = IntVar()
  53         OM1Val = StringVar()
  54         OM2Val = StringVar()
  55         CART = IntVar()
  56         OVERLAP = IntVar()
  57         NOSEARCHSC = IntVar()
  58         objects_list = ['Select object']
  59         seq_list=[]
  60         seq_length=0
  61
  62         weights = ['WLONG','WSCC','WSCP','WELEC','WVDWPP','WEL_LOC','WCORR4','WCORR5','WCORR6','WTURN3','WTURN4','WTURN6','WSCCOR','WSTRAIN','WBOND','WTOR','WTORD','WANG','WSCLOC','SCAL14','SCALSCP','WCORRH','CUTOFF' ]
  63
  64         force_fields = [ {'FF':'GAB', 'WLONG' :'1.35279', 'WSCP'   :'1.59304', 'WELEC' :'0.71534', 'WBOND' :'1.00000', 'WANG'  :'1.13873', 'WSCLOC':'0.16258', 'WTOR':'1.98599', 'WTORD':'1.57069', 'WCORRH':'0.42887', 'WCORR5':'0.00000',
  65                                         'WCORR6':'0.00000', 'WEL_LOC':'0.16036', 'WTURN3':'1.68722', 'WTURN4':'0.66230', 'WTURN6':'0.00000', 'WVDWPP':'0.11371', 'WHPB':'1.00000', 'WCORR4':'0.00000', 'CUTOFF':'7.00000'},
  66                     {'FF':'E0G', 'WLONG':'1.70905', 'WSCP':'2.18310', 'WELEC':'1.06684', 'WBOND':'1.00000', 'WANG':'1.17536', 'WSCLOC':'0.22070', 'WTOR':'2.65798', 'WTORD':'2.00646', 'WCORRH':'0.23541', 'WCORR5':'0.00000',
  67                                         'WCORR6':'0.00000', 'WEL_LOC':'0.42789', 'WTURN3':'1.68126', 'WTURN4':'0.75080', 'WTURN6':'0.00000', 'WVDWPP':'0.27044', 'WHPB':'1.00000', 'WSCP14':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000'},
  68                     {'FF':'1L2Y_1LE1', 'WLONG' :'1.00000', 'WSCP'    :'1.23315', 'WELEC' : '0.84476', 'WBOND' :'1.00000', 'WANG'  :'0.62954', 'WSCLOC': '0.10554', 'WTOR': '1.84316', 'WTORD' : '1.26571', 'WCORRH': '0.19212', 'WCORR5': '0.00000',
  69                                         'WCORR6':'0.00000', 'WEL_LOC':'0.37357', 'WTURN3':'1.40323', 'WTURN4':'0.64673', 'WTURN6':'0.00000', 'WVDWPP': '0.23173', 'WHPB': '1.00000', 'WSCCOR': '0.00000', 'CUTOFF': '7.00000', 'WCORR4': '0.00000'},
  70                     {'FF':'4P',  'WSC':'1.00000', 'WSCP':'2.73684', 'WELEC':'0.06833', 'WANG':'4.15526', 'WSCLOC':'0.16761', 'WTOR':'2.99546', 'WTORD':'2.89720', 'WCORRH':'1.98989', 'WCORR5':'0.00000', 'WCORR6':'0.00000', 'WEL_LOC':'1.60072',
  71                                         'WTURN3':'2.36351', 'WTURN4':'1.34051', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  72                     {'FF':'3P',  'WSC':'1.00000', 'WSCP':'2.85111', 'WELEC':'0.36281', 'WANG':'3.95152', 'WSCLOC':'0.15244', 'WTOR':'3.00008', 'WTORD':'2.89863', 'WCORRH':'1.91423', 'WCORR5':'0.00000', 'WCORR6':'0.00000', 'WEL_LOC':'1.72128',
  73                                         'WTURN3':'2.99827', 'WTURN4':'0.59174', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  74                         {'FF':'CASP5',          'WSC':'1.00000',        'WSCP':'1.54864', 'WELEC':'0.20016', 'WANG': '1.00572', 'WSCLOC': '0.06764', 'WTOR':'1.70537', 'WTORD':'1.24442', 'WCORRH':'0.91583', 'WCORR5':'0.00607', 'WCORR6':'0.02316', 'WEL_LOC':'1.51083',
  75                                         'WTURN3':'2.00764', 'WTURN4':'0.05345', 'WTURN6':'0.05282', 'WSCCOR':'0.0', 'CUTOFF': '7.00000', 'WCORR4':'0.00000' },
  76                         {'FF':'ALPHABETA',      'WSC':'1.00000', 'WSCP':'1.43178', 'WELEC':'0.41501', 'WANG':'0.37790', 'WSCLOC':'0.12880', 'WTOR':'1.98784', 'WCORRH':'2.50526', 'WCORR5':'0.23873', 'WCORR6':'0.76327', 'WEL_LOC':'2.97687', 'WTURN3':'0.09261',
  77                                         'WTURN4':'0.79171', 'WTURN6':'0.01074', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  78                         {'FF':'BETA', 'WSC':'1.00000', 'WSCP':'1.10684', 'WELEC':'0.70000', 'WANG':'0.80775', 'WSCLOC':'1.91939', 'WTOR':'3.36070', 'WCORRH':'2.50000', 'WCORR5':'0.99949', 'WCORR6':'0.46247', 'WEL_LOC':'2.50000', 'WTURN3':'1.80121',
  79                                         'WTURN4':'4.35377', 'WTURN6':'0.10000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  80                         {'FF':'ALPHA', 'WSC':'1.00000', 'WSCP':'0.72364', 'WELEC':'1.10890', 'WANG':'0.68702', 'WSCLOC':'1.79888', 'WTOR':'0.30562', 'WCORRH':'1.09616', 'WCORR5':'0.17452', 'WCORR6':'0.36878', 'WEL_LOC':'0.19508', 'WTURN3':'0.00000',
  81                                         'WTURN4':'0.55588', 'WTURN6':'0.11539', 'CUTOFF':'7.00000', 'WCORR4':'0.0000', 'WTORD':'0.00000', 'WSCCOR':'0.00000'},
  82                         {'FF':'CASP3', 'WELEC':'1.50000', 'WSTRAIN':'1.00000', 'WTOR':'0.08617', 'WANG':'0.10384', 'WSCLOC':'0.10384', 'WCORR':'1.50000', 'WTURN3':'0.00000', 'WTURN4':'0.00000', 'WTURN6':'0.00000', 'WEL_LOC':'0.00000', 'WCORR5':'0.00000',
  83                                         'WCORR6':'0.00000', 'SCAL14':'0.40000', 'SCALSCP':'1.00000', 'CUTOFF':'7.00000', 'WSCCOR':'0.00000'}
  84         ]
  85
  86         one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', 'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', 'GLY':'G', 'PRO':'P', 'CYS':'C'}
  87
  88
  89         def __init__(self,parent):
  90                 # Create the GUI window
  91                 root = Toplevel.__init__(self)
  92                 self.config(width=400, height=300)              # create a root window
  93                 self.title("UNRES Input Generator v"+UNRESInpGen_version)                 # Set window title
  94                 self.resizable(0, 0)                                # Disable window resize
  95                 self.geometry('-40+40')                             # Set window placement
  96
  97                 # Create the Balloon.
  98                 self.balloon = Pmw.Balloon(root)
  99
 100                 #================================
 101                 # "Main Options" group
 102                 #
 103                 self.gr1 = Pmw.Group(self,tag_text = 'Main options')
 104                 self.gr1.grid(row=0, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 105
 106                 # - Create title Entryfield & Label
 107                 #self.l1 = Label(self.gr1.interior(), text="Title:")
 108                 #self.l1.grid(row=0, column=0,sticky=E)
 109                 self.e1 = Pmw.EntryField(self.gr1.interior(),
 110                         labelpos='w',
 111                         label_text="Title:",
 112                         validate = {'max': 80 },
 113                 #       value ="(Place input information here)"
 114                 )
 115                 self.e1.component('entry').config(width=80)
 116                 self.e1.grid(row=0, column=0,columnspan=4, sticky=E)
 117
 118                 # - Create "choose method" OptionMenu
 119                 self.OM1Val.set('MD')
 120                 self.optmenu1 =  Pmw.OptionMenu(self.gr1.interior(),
 121                         labelpos = 'w',
 122                         label_text = 'Choose method:',
 123                         menubutton_textvariable = self.OM1Val,
 124                         items = ['MD', 'REMD/MREMD', 'MINIMIZE' ],
 125                         command = self.switch_options,
 126                         menubutton_width = 10
 127                 )
 128                 self.optmenu1.grid(row=1, column=0,columnspan=2, sticky=E)
 129
 130
 131                 # - Seed entryfield
 132                 self.gr1.e1 = Pmw.EntryField(self.gr1.interior(),
 133                         labelpos='w',
 134                         label_text="Seed",
 135                         validate = {'validator' : 'integer', 'min': -2147483648 , 'max' : 0 },
 136                         value = "-1111333"
 137                 )
 138                 self.gr1.e1.component('entry').config(width=8)
 139                 self.gr1.e1.grid(row=1, column=2, sticky=W)
 140
 141                 #==================================
 142                 # - MD options frame
 143                 #
 144                 self.gr1.md = Frame(self.gr1.interior())
 145                 self.gr1.md.grid(row=2, column=0, columnspan=4,sticky=W+E)
 146
 147                 # -- nstep entryfield
 148                 self.gr1.md.e1 = Pmw.EntryField(self.gr1.md,
 149                         labelpos='w',
 150                         label_text="NSTEP",
 151                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
 152                         value = "500000"
 153                 )
 154                 self.balloon.bind(self.gr1.md.e1,'Number of calculation steps')
 155                 self.gr1.md.e1.component('entry').config(width=8)
 156                 self.gr1.md.e1.grid(row=0, column=0, sticky=E)
 157
 158                 # -- ntwe entryfield
 159                 self.gr1.md.e2 = Pmw.EntryField(self.gr1.md,
 160                         labelpos='w',
 161                         label_text="NTWE",
 162                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 163                         value = "100"
 164                 )
 165                 self.balloon.bind(self.gr1.md.e2,'Frequency of energy output.\nNTWE=0 means no energy dump. ')
 166                 self.gr1.md.e2.component('entry').config(width=8)
 167                 self.gr1.md.e2.grid(row=0,column=1, sticky=E)
 168
 169                 # -- ntwx entryfield
 170                 self.gr1.md.e3 = Pmw.EntryField(self.gr1.md,
 171                         labelpos='w',
 172                         label_text="NTWX",
 173                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
 174                         value = "1000"
 175                 )
 176                 self.balloon.bind(self.gr1.md.e3, "Frequency of coordinate output.")
 177                 self.gr1.md.e3.component('entry').config(width=8)
 178                 self.gr1.md.e3.grid(row=0,column=2, sticky=E)
 179
 180                 # -- dt entryfield
 181                 self.gr1.md.e4 = Pmw.EntryField(self.gr1.md,
 182                         labelpos='w',
 183                         label_text="DT",
 184                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 185                         value = "0.1")
 186                 self.balloon.bind(self.gr1.md.e4, "Time step. \nThe unit is \"molecular time unit\" (mtu)\n 1 mtu = 48.9 fs")
 187                 self.gr1.md.e4.component('entry').config(width=8)
 188                 self.gr1.md.e4.grid(row=0,column=3, sticky=E)
 189
 190                 # -- damax entryfield
 191                 self.gr1.md.e5 = Pmw.EntryField(self.gr1.md,
 192                         labelpos='w',
 193                         label_text="DAMAX",
 194                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 195                         value = "1.0")
 196                 self.balloon.bind(self.gr1.md.e5, "Maximum allowed change of acceleration during a single time step.\nThe time step gets scaled down, if this is exceeded.")
 197                 self.gr1.md.e5.component('entry').config(width=8)
 198                 self.gr1.md.e5.grid(row=1,column=0, sticky=E)
 199
 200                 # -- dvmax entryfield
 201                 self.gr1.md.e6 = Pmw.EntryField(self.gr1.md,
 202                         labelpos='w',
 203                         label_text="DVMAX",
 204                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 205                         value = "20.0")
 206                 self.balloon.bind(self.gr1.md.e6, "Maximum allowed velocity (in A/mtu).")
 207                 self.gr1.md.e6.component('entry').config(width=8)
 208                 self.gr1.md.e6.grid(row=1,column=1, sticky=E)
 209
 210                 # -- restet_vel entryfield
 211                 self.gr1.md.e7 = Pmw.EntryField(self.gr1.md,
 212                         labelpos='w',
 213                         label_text="RESET_VEL",
 214                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 10000000 },
 215                         value = "1000")
 216                 self.balloon.bind(self.gr1.md.e7, "Frequency of resetting velocities to values from Gaussian distribution")
 217                 self.gr1.md.e7.component('entry').config(width=8)
 218                 self.gr1.md.e7.grid(row=1,column=2, sticky=E)
 219
 220                 # -- initial structure
 221                 self.gr1.md.om1 = Pmw.OptionMenu(self.gr1.md,
 222                         labelpos = 'w',
 223                         label_text = 'Start from',
 224                         items = ['PDB', 'extended', 'random' ],
 225                         menubutton_width = 8,
 226                 )
 227                 self.gr1.md.om1.grid(row=1,column=3, sticky=E)
 228
 229                 #=================================
 230                 #  - thermostat frame
 231                 #
 232                 self.gr1.th = Frame(self.gr1.interior())
 233                 self.gr1.th.grid(row=3, column=0, columnspan=5,sticky=W+E)
 234
 235                 # -- Thermostat optionmenu
 236                 self.gr1.th.optmenu1 =  Pmw.OptionMenu(self.gr1.th,
 237                         labelpos = 'w',
 238                         label_text = 'thermostat',
 239                         items = ['Berendsen', 'Nose-Poincare 1999','Nose-Poincare 2001', 'Nose-Hoover', 'Langevin' ],
 240                         command=self.set_thermostat,
 241                         menubutton_width = 15
 242                 )
 243                 self.gr1.th.optmenu1.pack(side=LEFT)#grid(row=0, column=0, sticky=E)
 244
 245                 # -- t_bath entryfield
 246                 self.gr1.th.e1 = Pmw.EntryField(self.gr1.th,
 247                         labelpos='w',
 248                         label_text="T_BATH",
 249                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 10000 },
 250                         value = "300.0")
 251                 self.balloon.bind(self.gr1.th.e1, "Temperature (in K) of canonical simulation.")
 252                 self.gr1.th.e1.component('entry').config(width=8)
 253                 self.gr1.th.e1.pack(side=LEFT)
 254
 255                 # -- tau_bath entryfield
 256                 self.gr1.th.e2 = Pmw.EntryField(self.gr1.th,
 257                         labelpos='w',
 258                         label_text="TAU_BATH",
 259                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
 260                         value = "1.0")
 261                 self.balloon.bind(self.gr1.th.e2, "(units are mtus; 1mtu=48.9 fs) \nConstant of the coupling to the thermal bath")
 262                 self.gr1.th.e2.component('entry').config(width=8)
 263                 self.gr1.th.e2.pack(side=LEFT)
 264
 265                 # -- q_np entryfield
 266                 self.gr1.th.e3 = Pmw.EntryField(self.gr1.th,
 267                         labelpos='w',
 268                         label_text="Q_NP",
 269                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
 270                         value = "0.1")
 271                 self.balloon.bind(self.gr1.th.e3, "Mass of the fictitious particle in the calculations with the Nose-Poincare & Nose-Hoover thermostats.")
 272                 self.gr1.th.e3.component('entry').config(width=8)
 273                 #self.gr1.th.e2.pack(side=LEFT)
 274
 275
 276                 #=================================
 277                 # - Minimization frame
 278                 self.gr1.mi = Frame(self.gr1.interior())
 279                 #self.gr1.mi.grid(row=4, column=0, columnspan=5,sticky=W+E)
 280
 281                 self.gr1.mi.e1 = Pmw.EntryField(self.gr1.mi,
 282                         labelpos='w',
 283                         label_text="MAXMIN",
 284                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 285                         value = "2000" )
 286                 self.balloon.bind(self.gr1.mi.e1,'Maximum number of iterations of the SUMSL minimizer.')
 287                 self.gr1.mi.e1.component('entry').config(width=8)
 288                 self.gr1.mi.e1.pack(side=LEFT)
 289
 290                 self.gr1.mi.e2 = Pmw.EntryField(self.gr1.mi,
 291                         labelpos='w',
 292                         label_text="MAXFUN",
 293                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 294                         value = "5000" )
 295                 self.balloon.bind(self.gr1.mi.e2,'Maximum number of function evaluations in a single minimization.')
 296                 self.gr1.mi.e2.component('entry').config(width=8)
 297                 self.gr1.mi.e2.pack(side=LEFT)
 298
 299                 self.gr1.mi.c1 = Checkbutton(self.gr1.mi,
 300                         text = "CART",
 301                         variable = self.CART )
 302                 self.balloon.bind(self.gr1.mi.c1,'Minimize in virtual-bond vectors instead of angles.')
 303                 self.gr1.mi.c1.pack(side=LEFT)
 304
 305                 self.gr1.mi.c2 = Checkbutton(self.gr1.mi,
 306                         text = "OVERLAP",
 307                         variable = self.OVERLAP )
 308                 self.balloon.bind(self.gr1.mi.c2,'Fix overlaping sidechains.')
 309                 self.gr1.mi.c2.pack(side=LEFT)
 310
 311                 self.gr1.mi.c3 = Checkbutton(self.gr1.mi,
 312                         text = "NOSEARCHSC",
 313                         variable = self.NOSEARCHSC )
 314                 #self.balloon.bind(self.gr1.mi.c3,'Minimize in virtual-bond vectors instead of angles.')
 315                 self.gr1.mi.c3.pack(side=LEFT)
 316
 317
 318                 #=================================
 319                 # - REMD frame
 320                 self.gr1.re = Frame(self.gr1.interior())
 321                 #self.gr1.re.grid(row=5, column=0, columnspan=5,sticky=W+E)
 322
 323                 self.gr1.re.e1 = Pmw.EntryField(self.gr1.re,
 324                         labelpos = 'w',
 325                         label_text = "NREP",
 326                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 32 },
 327                         command = self.set_replica_widgets,
 328                         value = "16" )
 329                 self.balloon.bind(self.gr1.re.e1,'Number of replicas in a REMD/MREMD run.')
 330                 self.gr1.re.e1.component('entry').config(width=8)
 331                 self.gr1.re.e1.grid(row=0, column=0, sticky=W)
 332
 333                 self.gr1.re.e2 = Pmw.EntryField(self.gr1.re,
 334                         labelpos = 'w',
 335                         label_text = "NSTEX",
 336                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 337                         value = "1000" )
 338                 self.balloon.bind(self.gr1.re.e2,'Number of steps after which exchange is performed in REMD/MREMD runs.')
 339                 self.gr1.re.e2.component('entry').config(width=8)
 340                 self.gr1.re.e2.grid(row=0, column=1, sticky=W)
 341
 342                 # -- radio select
 343                 self.gr1.re.rs = Pmw.RadioSelect(self.gr1.re,
 344                         labelpos = 'w',
 345                         label_text = 'Replica temperatures',
 346                         command = self.sel_replica_mode,
 347                         buttontype = 'radiobutton'
 348                         #frame_borderwidth = 2,
 349                         #frame_relief = 'ridge'
 350                         )
 351                 self.gr1.re.rs.grid(row=1, column=0, columnspan=4,sticky=W)
 352
 353                 for text in ('Manual', 'Range'):
 354                         self.gr1.re.rs.add(text)
 355
 356                 # --- range
 357                 self.gr1.re.tf1 = Frame(self.gr1.re, bg="blue")
 358                 self.gr1.re.tf1.grid(row=2,column=0, columnspan=4, sticky=W)
 359
 360                 self.gr1.re.tf1.e1 = Pmw.EntryField(self.gr1.re.tf1,
 361                         labelpos = 'w',
 362                         label_text = "RETMIN",
 363                         validate = {'validator' : 'real', 'min': 0 , 'max' : 1000000 },
 364                         value = "10" )
 365                 self.balloon.bind(self.gr1.re.tf1.e1,'Minimum temperature in a REMD/MREMD run.')
 366                 self.gr1.re.tf1.e1.component('entry').config(width=8)
 367                 self.gr1.re.tf1.e1.grid(row=0, column=0, sticky=W)
 368
 369                 self.gr1.re.tf1.e2 = Pmw.EntryField(self.gr1.re.tf1,
 370                         labelpos = 'w',
 371                         label_text = "RETMAX",
 372                         validate = {'validator' : 'real', 'min': 0 , 'max' : 1000000 },
 373                         value = "1000" )
 374                 self.balloon.bind(self.gr1.re.tf1.e2,'Maxmum temperature in a REMD/MREMD run.')
 375                 self.gr1.re.tf1.e2.component('entry').config(width=8)
 376                 self.gr1.re.tf1.e2.grid(row=0, column=1, sticky=W)
 377
 378                 # --- manual
 379                 self.gr1.re.tf2 = Frame(self.gr1.re)
 380                 self.gr1.re.tf2.grid(row=3,column=0, columnspan=4, sticky=W)
 381
 382                 self.gr1.re.tf2.te = []
 383                 for i in range(0,32): #int(self.gr1.re.e1.get())):
 384                         self.gr1.re.tf2.te.append(Pmw.EntryField(self.gr1.re.tf2,
 385                                 labelpos='n',
 386                                 label_text='T%02d' % (i+1),
 387                                 validate = {'validator' : 'real','min' : 0, 'max' : 1000, 'minstrict' : 0},
 388                                 value = '%d' % (200+i*10)))
 389                         self.gr1.re.tf2.te[i].component('entry').config(width=3)
 390                         self.gr1.re.tf2.te[i].grid(row=1+(i//16), column=0+(i % 16))
 391
 392                 self.gr1.re.tf2.nre = Pmw.EntryField(self.gr1.re.tf2,
 393                         labelpos ='n',
 394                         label_text='Rep. in Temp.',
 395                         validate = {'validator' : 'integer','min' : 1, 'max' : 100 },
 396                         value = '2')
 397                 self.gr1.re.tf2.nre.component('entry').config(width=3)
 398                 self.gr1.re.tf2.nre.grid(row=1, column=17)
 399
 400                 # display manual replica options
 401                 self.gr1.re.e1.invoke()
 402                 self.gr1.re.rs.invoke('Manual')
 403
 404                 #=================================
 405                 # "Force field options" group
 406                 #
 407                 self.gr2 = Pmw.Group(self,tag_text = 'Force field options')
 408                 self.gr2.grid(row=2, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 409
 410                 # - Create "force field parameters" Option menu
 411                 self.OM2Val.set('Custom')
 412                 self.optmenu2 = Pmw.OptionMenu(self.gr2.interior(),
 413                 label_text = 'Force field parameters:',
 414                         labelpos = 'w',
 415                         menubutton_textvariable = self.OM2Val,
 416                         items = ['Custom','GAB','E0G', '1L2Y_1LE1','4P','3P','CASP5','ALPHABETA','BETA','ALPHA','CASP3' ],
 417                         initialitem = 'Custom',
 418                         menubutton_width = 10,
 419                         command=self.set_force_field
 420                 )
 421                 self.optmenu2.grid(row=0, column=0,columnspan=4,sticky=E)
 422
 423                 # Force field parameters Entry Fields
 424                 self.ef = []
 425                 for i in range(0,len(self.weights)):
 426                         self.ef.append(Pmw.EntryField(self.gr2.interior(),
 427                         labelpos='n',
 428                         label_text=self.weights[i],
 429                         validate = {'validator' : 'real','min' : 0, 'max' : 10, 'minstrict' : 0},
 430                         value = '1.00000'))
 431                         self.ef[i].component('entry').config(width=8)
 432                         self.ef[i].grid(row=1+(i//9), column=0+(i % 9))
 433
 434                 #===================================
 435                 # "Sequence" group
 436                 #
 437                 self.gr3 = Pmw.Group(self,tag_text = 'Sequence')
 438                 self.gr3.grid(row=3, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 439
 440                 self.gr3.f1 = Frame(self.gr3.interior())
 441                 # Object List
 442                 self.cb2 = Pmw.ComboBox(self.gr3.f1,
 443                         labelpos = 'w',
 444                         #entry_relief = 'raised',
 445                         label_text = 'Selection/Object',
 446                         scrolledlist_items = self.objects_list
 447                 )
 448                 self.cb2.pack(side=LEFT)
 449                 # refresh button
 450                 self.gr3.btn1 = Button(self.gr3.f1, text='Refresh', padx=0, pady=0 , command = self.refresh_list)
 451                 self.gr3.btn1.pack(side=LEFT)
 452                 # Get sequence button
 453                 self.gr3.btn2 = Button(self.gr3.f1, text='Get Sequence', padx=0, pady=0 , command = self.get_seq)
 454                 self.gr3.btn2.pack(side=LEFT)
 455
 456                 self.gr3.f1.pack(expand="yes",fill="both")
 457
 458                 # Disulfide brige checkbox
 459                 self.gr3.chk = Checkbutton(self.gr3.f1, text="Write disulfide bridges", variable=self.writeSSbrige)
 460                 self.gr3.chk.pack(side=LEFT)
 461
 462                 # Sequence text
 463                 self.gr3.t1 = Pmw.ScrolledText(self.gr3.interior(),
 464                         columnheader = 1,
 465                         columnheader_width = 3,
 466                         rowheader = 1,
 467                         rowheader_width = 4,
 468                         usehullsize=1,
 469                         hull_width=30,
 470                         hull_height=180,
 471                         text_padx = 4,
 472                         text_pady = 4,
 473                         Header_padx = 4,
 474                         rowheader_pady = 4,
 475                 )
 476                 # Sequence text - create the header line
 477                 headerline = ''
 478                 for column in range(1,21):
 479                         headerline = headerline + ('%-4s' % str(column) )
 480                 self.gr3.t1.component('columnheader').insert('0.0',headerline)
 481
 482                 self.gr3.t1.pack(expand="yes",fill="both")
 483
 484                 # Add some buttons
 485                 btn3=Button(self, text='Write Input', padx=0, pady=0, command = self.ok)
 486                 btn3.grid(row=10, column=0, columnspan=2,sticky=N+W+S+E)
 487                 btn4=Button(self, text='Close', padx=0, pady=0, command = self.myHide)
 488                 btn4.grid(row=10, column=2, columnspan=2,sticky=N+W+S+E)
 489
 490                 # create callback to prevent window kill
 491                 self.protocol("WM_DELETE_WINDOW", self.myHide)
 492
 493         def ToggleColor(self):
 494                 if self.colorize.get()==1:
 495                         for i in range(0,len(self.res_states)):
 496                                 UNRESInpGenWindow.ccb[i].config(state=ACTIVE, bg=self.res_states[i][1], activebackground=self.res_states[i][1], relief=RAISED, overrelief=RAISED)
 497                 else:
 498                         for i in range(0,len(self.res_states)):
 499                                 UNRESInpGenWindow.ccb[i].config(state=DISABLED, bg=self.Default_Color , activebackground=self.Default_Color, relief=RAISED, overrelief=RAISED)
 500
 501         def myShow(self):
 502                 self.deiconify()
 503
 504         def myHide(self):
 505                 self.withdraw()
 506
 507         def myToggle(self):
 508                 if self.state() == "normal":
 509                         self.myHide()
 510                 elif self.state() == "withdrawn":
 511                         self.myShow()
 512
 513         def get_selections(self):
 514                 self.objects_list = []
 515                 for item in cmd.get_names("all"):
 516                         if cmd.get_type(item)=="object:molecule":
 517                                 self.objects_list.append(item)
 518                         if cmd.get_type(item)=="selection":
 519                                 if item[0]<>"_":
 520                                         self.objects_list.append(item)
 521
 522         def get_nonstandard(self):
 523                 stored.list=[]
 524                 cmd.iterate("(all)","stored.list.append(resn)")
 525                 stored.list=list(Set(stored.list))  # remove duplicates
 526                 # Remove standard amino acids and water from list
 527                 for m in ['HIS','ASP','ARG','PHE','ALA','CYS','GLY','GLN','GLU','LYS','LEU','MET','ASN','SER','TYR','THR','ILE','TRP','PRO','VAL','HOH']:
 528                         try:
 529                                 stored.list.remove(m)
 530                         except ValueError:
 531                                 pass
 532                 UNRESInpGenWindow.cbcr1.setlist(stored.list)
 533
 534         def refresh_list(self):
 535                 # Save old values
 536                 old = self.objects_list
 537                 try:
 538                         old_cb2=self.cb2.getvalue()[0]
 539                 except:
 540                         old_cb2=''
 541                 self.get_selections()
 542
 543                 # Update selectionlist if needed
 544                 if not(old==self.objects_list):
 545                         self.cb2.setlist(self.objects_list)
 546                         self.cb2.setlist(self.objects_list)
 547
 548                 if not(old_cb2 in self.objects_list):
 549                         # No - clear the combobox entry
 550                         self.cb2.component('entryfield').clear()
 551                 else:
 552                         # Yes - set the old value
 553                         self.cb2.selectitem(old_cb2,setentry=1)
 554
 555
 556         def get_seq(self):
 557                 # Get the number of chains
 558                 try:
 559                         nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
 560                 except:
 561                         nchains=0
 562                 pass
 563
 564                 if (nchains>0):
 565                         self.seq_list=[]
 566                 offset=0
 567                 seq_data=''
 568                 self.seq_length=0
 569                 for chain in range(0,nchains):
 570                         # Get only amonoacids, N-terminus acyl and C-terminus amide
 571                         # example:      (1uRC and chain F and (n. ca or (resn ACE and n. C) or (resn NH2 and n. N)))
 572                         # No chain information or only one chain
 573                         if nchains==1:
 574                                 atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
 575                         # Chain information is present
 576                         else:
 577                                 atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & chain "+cmd.get_chains(self.cb2.getvalue()[0])[chain]+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
 578                         # dodaj separator lancuchow
 579                         if chain>0:
 580                                 self.seq_list.append("D  ")
 581                                 self.seq_length+=1
 582
 583
 584                         # Zamiana chronionych
 585                         # ACE ALA ALA NH2 D   ACE ALA ALA NH2
 586                         # GLY ALA ALA GLY D   GLY ALA ALA GLY
 587                         # Zamiana niechronionych
 588                         #     ALA ALA     D       ALA ALA
 589                         # D   ALA ALA     D       ALA ALA D
 590                         #
 591                         # j - licznik pozycji reszty
 592                         j=0
 593                         for i in atomchain:
 594                                 self.seq_length+=1
 595                                 if str(i.resn)=="NH2":
 596                                         self.seq_list.append("GLY")
 597                                 elif str(i.resn)=="NHH":
 598                                         self.seq_list.append("GLY")
 599                                 elif str(i.resn)=="NME":
 600                                         self.seq_list.append("GLY")
 601                                 elif str(i.resn)=="ACE":
 602                                         self.seq_list.append("GLY")
 603                                 elif str(i.resn)=="GLY":
 604                                         self.seq_list.append("GLY")
 605                                 else:
 606                                         if j==0 and chain==0:
 607                                                 self.seq_list.append("D  ")
 608                                                 self.seq_list.append(str(i.resn))
 609                                                 self.seq_length+=1
 610                                         elif j==len(atomchain)-1 and chain==(nchains-1):
 611                                                 self.seq_list.append(str(i.resn))
 612                                                 self.seq_list.append("D  ")
 613                                                 self.seq_length+=1
 614                                         else:
 615                                                 self.seq_list.append(str(i.resn))
 616                                 j+=1
 617                 rows=0
 618                 #row_header='0'  - old header
 619                 row_header='1'
 620                 # tag setup
 621                 self.gr3.t1.tag_configure('dummy', background = 'LightBlue1')
 622                 tagList=[]
 623                 self.gr3.t1.tag_configure('cysteine', background = 'LightGoldenrod1')
 624                 CysTagList=[]
 625
 626                 for i in range(len(self.seq_list)):
 627                         # Dummy tag
 628                         if self.seq_list[i]=="D  ":
 629                                 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
 630                                 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
 631                                 tagList.append(tag1)
 632                                 tagList.append(tag2)
 633                         # Cysteine tag
 634                         if self.seq_list[i]=="CYS" or self.seq_list[i]=="CYX":
 635                                 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
 636                                 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
 637                                 CysTagList.append(tag1)
 638                                 CysTagList.append(tag2)
 639                         #
 640                         offset+=1
 641                         seq_data=seq_data+self.seq_list[i]+" "
 642                         # Line Wrap
 643                         if offset>19:
 644                                 offset=0
 645                                 seq_data=seq_data+'\n'
 646                                 rows+=1
 647                                 #row_header=row_header+'\n'+str(rows*20)    - old header
 648                                 row_header=row_header+'\n'+str(rows+1)
 649
 650                 self.gr3.t1.clear()
 651                 self.gr3.t1.insert('end',seq_data)
 652                 # Apply tags
 653                 if len(tagList):
 654                         apply(self.gr3.t1.tag_add, ('dummy',) + tuple(tagList))
 655                 if len(CysTagList):
 656                         apply(self.gr3.t1.tag_add, ('cysteine',) + tuple(CysTagList))
 657
 658                 # Show row header
 659                 self.gr3.t1.component('rowheader').delete(1.0, END)
 660                 self.gr3.t1.component('rowheader').insert('end',row_header)
 661
 662
 663         def switch_options(self,calctype):
 664                 '''
 665                         Displays the options available to set depending on the currently
 666                         selected calculation type
 667                 '''
 668                 # Hide all
 669                 self.gr1.th.grid_remove()
 670                 self.gr1.md.grid_remove()
 671                 self.gr1.mi.grid_remove()
 672                 self.gr1.re.grid_remove()
 673                 # Show MD stuff
 674                 if  self.OM1Val.get()=="MD":
 675                         self.gr1.md.grid(row=2, column=0, columnspan=5, sticky=W+E)
 676                         self.gr1.th.grid(row=3, column=0, columnspan=5, sticky=W+E)
 677                 elif self.OM1Val.get()=="REMD/MREMD":
 678                         self.gr1.md.grid(row=2, column=0, columnspan=5, sticky=W+E)
 679                         self.gr1.th.grid(row=3, column=0, columnspan=5, sticky=W+E)
 680                         self.gr1.re.grid(row=5, column=0, columnspan=5, sticky=W+E)
 681                 elif self.OM1Val.get()=="MINIMIZE":
 682                         self.gr1.mi.grid(row=4,column=0,columnspan=5, sticky=W+E)
 683
 684         def sel_replica_mode(self,mode):
 685                 '''
 686                         Display replica temperatures settings
 687                 '''
 688                 try:
 689                         self.gr1.re.tf1.grid_remove()
 690                         self.gr1.re.tf2.grid_remove()
 691                         if mode=="Range":
 692                                 self.gr1.re.tf1.grid(row=2,column=0, columnspan=4, sticky=W)
 693                         elif mode=="Manual":
 694                                 self.gr1.re.tf2.grid(row=3,column=0, columnspan=4, sticky=W)
 695                 except:
 696                         pass
 697
 698         def set_replica_widgets(self):
 699                 '''
 700                         Refresh list of available temperature widgets in manual mode
 701                 '''
 702                 #print self.gr1.re.e1.get()
 703                 for i in range(0,32): #int(self.gr1.re.e1.get())):
 704                         try:
 705                                 if i<int(self.gr1.re.e1.get()):
 706                                         self.gr1.re.tf2.te[i].component('entry').config(state=NORMAL)
 707                                 else:
 708                                         self.gr1.re.tf2.te[i].component('entry').config(state=DISABLED)
 709                         except:
 710                                 pass
 711
 712
 713
 714         def set_force_field(self, pole):
 715                 '''
 716                         Enables/disables entryfields for force field perameters depending
 717                         on the currently selected force field
 718                 '''
 719                 for ff in self.force_fields:
 720                         if ff['FF']==pole:
 721                                 #print ff
 722                                 for i in range(0,len(self.weights)):
 723                                         if ff.has_key(self.weights[i]):
 724                                                 self.ef[i].setvalue(ff.get(self.weights[i]))
 725                                                 self.ef[i].component('entry').config(state=NORMAL)
 726                                         else:
 727                                                 self.ef[i].component('entry').config(state=DISABLED)
 728                         # Custom force field
 729                         elif pole=='Custom':
 730                                 for i in range(0,len(self.weights)):
 731                                         self.ef[i].component('entry').config(state=NORMAL)
 732
 733         def set_thermostat(self,thermostat):
 734                 '''
 735                         Display additional widget acording to selected thermostat
 736                 '''
 737                 #print thermostat
 738                 self.gr1.th.e2.pack_forget()
 739                 self.gr1.th.e3.pack_forget()
 740                 if thermostat=='Berendsen':
 741                         self.gr1.th.e2.pack(side=LEFT)
 742                 elif thermostat=='Nose-Poincare 1999' or thermostat=='Nose-Poincare 2001' or thermostat=='Nose-Hoover':
 743                         self.gr1.th.e3.pack(side=LEFT)
 744
 745         def fortran_format(self,s):
 746                 '''
 747                     Formats string containing keywords to wrap over 80 columns.
 748                         Input string should be one line.
 749                 '''
 750                 tmpstr=''
 751                 column=1
 752                 for k in s.split():
 753                         if column+len(k)+1<80:
 754                                 tmpstr+=k+' '
 755                                 column+=len(k)+1
 756                         else:
 757                                 tmpstr+=" "*(80-column)+"&\n"+k+" "
 758                                 column=len(k)+2
 759                 tmpstr+='\n'
 760                 return tmpstr
 761
 762         def get_weights(self):
 763                 '''
 764                         Get the force field weights
 765                 '''
 766                 s = ''
 767                 for i in range(0,len(self.weights)):
 768                         if self.ef[i].component('entry').cget("state")=="normal":
 769                                 s+=self.weights[i]+"="+self.ef[i].getvalue()+" "
 770                 return s
 771
 772         def get_md_opt(self):
 773                 '''
 774                         Get MD options for main input
 775                 '''
 776                 s = "NSTEP="+self.gr1.md.e1.getvalue()+" NTWE="+self.gr1.md.e2.getvalue()+" "
 777                 s+= "NTWX="+self.gr1.md.e3.getvalue()+" DT="+self.gr1.md.e4.getvalue()+" "
 778                 s+= "DAMAX="+self.gr1.md.e5.getvalue()+" DVMAX="+self.gr1.md.e6.getvalue()+" "
 779                 s+= "RESET_VEL="+self.gr1.md.e7.getvalue()+" "
 780
 781                 # Thermostat options
 782                 term=self.gr1.th.optmenu1.getvalue()
 783                 #print term
 784                 if term=="Berendsen":
 785                         s+="TBF TAU_BATH="+self.gr1.th.e2.getvalue()+" "
 786                 elif term=="Nose-Poincare 1999":
 787                         s+="NOSEPOINCARE99 Q_NP="+self.gr1.th.e3.getvalue()+" "
 788                 elif term=="Nose-Poincare 2001":
 789                         s+="NOSEPOINCARE01 Q_NP="+self.gr1.th.e3.getvalue()+" "
 790                 elif term=="Nose-Hoover":
 791                         s+="NOSEHOOVER96 Q_NP="+self.gr1.th.e3.getvalue()+" "
 792                 elif term=="Langevin":
 793                         s+="LANG=1 "
 794
 795                 s+="T_BATH="+self.gr1.th.e1.getvalue()+" "
 796                 return s
 797
 798         def get_minim_opt(self):
 799                 '''
 800                         Get minimization options
 801                 '''
 802                 s = "MAXMIN="+self.gr1.mi.e1.getvalue()+" MAXFUN="+self.gr1.mi.e2.getvalue()
 803                 return s
 804
 805
 806         def get_mremd_opt(self):
 807                 '''
 808                         Generates a sting containing REMD?MREMD main options for input
 809                 '''
 810                 s = "NREP="+self.gr1.re.e1.get()+" NSTEX="+self.gr1.re.e2.get()+" "
 811                 if self.gr1.re.rs.getvalue()=="Range":
 812                         s+="RETMIN="+self.gr1.re.tf1.e1.get()+"RETMAX="+self.gr1.re.tf1.e2.get()
 813                 else:
 814                         s+="TLIST MLIST"
 815                 s+=" TRAJ1FILE REST1FILE SYNC"
 816
 817                 return s
 818
 819         def get_mremd_temp_opt(self):
 820                 '''
 821                         Generate a strong containing temperatures for REMD/MREMD "manual mode"
 822                 '''
 823                 s=""
 824                 for i in range(0,int(self.gr1.re.e1.get())):
 825                         s+=self.gr1.re.tf2.te[i].get()+" "
 826
 827                 return s
 828
 829         def get_mremd_replicas(self):
 830                 '''
 831                         Generates a string containing number of replicas in every temperature for REMD/MREMD calculations.
 832                         For REMD calculations contains only sequence of ones.
 833                 '''
 834                 s=""
 835                 for i in range(0,int(self.gr1.re.e1.get())):
 836                         s+=self.gr1.re.tf2.nre.get()+" "
 837                 return s
 838
 839
 840         def get_seq_data(self):
 841                 '''
 842                         Dumps the sequence and disulfide bridge information
 843                 '''
 844                 # write sequence length
 845                 s = str(self.seq_length)+"\n"
 846
 847                 chains=cmd.get_chains(self.cb2.getvalue()[0])
 848                 nchains=len(chains)
 849
 850                 # apply one space before each sequence line
 851                 seq=self.gr3.t1.get()
 852                 for line in seq.split('\n'):
 853                         s+=" "+line+"\n"
 854                 # remove last newline character
 855                 s = s[:-1]
 856
 857                 # disulfide bridges - get half-cysteines by selection:
 858         # sele (bto. ((object) & r. CYS+CYX & n. SG) )& n. SG
 859                 ncys=cmd.get_model("(bto. (("+str(self.cb2.getvalue()[0])+") & r. CYS+CYX & n. SG)) & n. SG").atom
 860                 nSSbr=len(ncys)/2
 861
 862
 863                 # Is "Write disulfide brige" checked?
 864                 # yes
 865                 if self.writeSSbrige.get():
 866                         # write number of half-cysteines
 867                         s+=str(len(ncys))+"\n"
 868                         if len(ncys)==0:
 869                                 # No half-cysteines, cys position = 0
 870                                 s+=" 0\n"
 871                         else:
 872                                 # Write half-cysteine positions in sequence
 873                                 #
 874                                 # get first chain
 875                                 first=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+str(chains[0])+" & n. ca")
 876
 877                                 # calculate base offset in first chain (if dummy atom present offset = 1 )
 878                                 if first.atom[0].resn=="GLY":
 879                                         boff=0
 880                                 else:
 881                                         boff=1
 882
 883                                 # create dictionary of PDB chain/resi to UNRES_index
 884                                 unresidx={}
 885                                 for c in ncys:
 886                                         # calculate residue index offset from first residue in chain containing half-cysteine
 887                                         fresinchain=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+c.chain+" & n. ca").atom
 888                                         roff=int(c.resi)-int(fresinchain[0].resi)+1
 889
 890                                         resb=0
 891                                         coff=0
 892                                         for r in chains:
 893                                                 if c.chain==r:
 894                                                         break
 895                                                 resb+=len(cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+r+" & n. ca").atom)
 896                                                 coff+=1
 897                                         # add key/value to dictionary
 898                                         unresidx[c.chain+"/"+str(c.resi)]=boff+resb+coff+roff
 899                                         s+=" "+str(boff+resb+coff+roff)
 900                                 s+="\n"
 901
 902                                 # Write the number of disulfide bridges
 903                                 s+=" "+str(nSSbr)+"\n"
 904
 905                                 lista_mostkow=[]
 906                                 for c in ncys:
 907                                         # get neibhoring Sulfur atom
 908                                         opis=c.chain+str(c.resi)
 909                                         lista_mostkow.append(opis)
 910                                         nbr=cmd.get_model("(bto. ("+str(self.cb2.getvalue()[0])+" & resi "+str(c.resi)+"& n. SG & chain "+str(c.chain)+")) & n. SG").atom[0]
 911                                         opis2=nbr.chain+str(nbr.resi)
 912                                         if opis2 not in lista_mostkow:
 913                                                 # Write witch half-cysteines build the i-th disulfide bridge
 914                                                 s+=" "+str(unresidx[c.chain+"/"+str(c.resi)])+" "+str(unresidx[nbr.chain+"/"+str(nbr.resi)])+"\n"
 915                                                 #print c.chain, c.resn,c.resi,"-S-S-", nbr.chain, nbr.resn,nbr.resi
 916                 # Don't writeSSbrige
 917                 else:
 918                         s+="0\n 0\n"
 919
 920                 return s
 921
 922
 923         def write_cshell(self, cshname,prefix):
 924                 '''
 925                         Writes the C-shell script needed to run UNRES calculations
 926                 '''
 927                 s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py\n#\n'
 928
 929                 # number of processors per energy
 930                 if self.OM1Val.get()=="MD":
 931                         s+='setenv FGPROCS 1\n'
 932
 933                 # Potential
 934                 if self.OM2Val.get()=="CASP3":
 935                         s+='setenv POT LJ\n'
 936                 else:
 937                         s+='setenv POT GB\n'
 938
 939                 # input file
 940                 s+='setenv PREFIX '+prefix+'\n'
 941
 942                 # Parallel stuff
 943                 s+='setenv OUT1FILE YES\n'
 944
 945                 # force filed parameters
 946                 s+='#---------------------------------------------------------------------\n'
 947                 s+='setenv DD $UNRES_ROOT/PARAM\n'
 948
 949                 if self.OM2Val.get()=="CASP3":
 950                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 951                         s+='setenv TORPAR $DD/torsion_cryst.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_LJ.parm\n'
 952                         s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\n'
 953                         s+='setenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 954                 elif self.OM2Val.get()=="ALPHA" or self.OM2Val.get()=="BETA" or self.OM2Val.get()=="ALPHABETA":
 955                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 956                         s+='setenv TORPAR $DD/torsion_ecepp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
 957                         s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 958                 elif self.OM2Val.get()=="CASP5":
 959                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 960                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
 961                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_iter7n_c\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 962                 elif self.OM2Val.get()=="3P":
 963                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 964                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.3P7_iter81_1r\n'
 965                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 966                 elif self.OM2Val.get()=="4P":
 967                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 968                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.4P5_iter33_3r\n'
 969                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 970                 elif self.OM2Val.get()=="GAB":
 971                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 972                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k\n'
 973                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 974                 elif self.OM2Val.get()=="E0G":
 975                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 976                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc\n'
 977                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 978                 elif self.OM2Val.get()=="1L2Y_1LE1":
 979                         s+='setenv BONDPAR $DD/bond_AM1.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm\n'
 980                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_$POT.parm\n'
 981                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 982                 elif self.OM2Val.get()=="Custom":
 983                         s+='setenv BONDPAR $DD/.parm\nsetenv THETPAR $DD/.parm\nsetenv ROTPAR $DD/.parm\n'
 984                         s+='setenv TORPAR $DD/.parm\nsetenv TORDPAR $DD/.parm\nsetenv SIDEPAR $DD/.parm\n'
 985                         s+='setenv ELEPAR $DD/.parm\nsetenv SCPPAR $DD/.parm\nsetenv FOURIER $DD/.parm\nsetenv SCCORPAR $DD/.parm\n'
 986
 987
 988
 989                 s+='setenv PATTERN $DD/patterns.cart\n'
 990                 s+='#---------------------------------------------------------------------\n'
 991                 s+='$UNRES_BIN $*\n'
 992
 993                 f = open(cshname, 'w')
 994                 f.write(s)
 995                 f.close()
 996
 997
 998         def setenv_info(self):
 999                 print '''IMPORTANT: Remember to set the following envirament variables for your shell before starting calculations:
1000                   UNRES_ROOT - the root directory where UNRES is installed on your system (should contain PARAM directory)
1001                   UNRES_BIN  - the UNRES binary you want to execute
1002                 '''
1003
1004
1005         def ok(self):
1006                 '''
1007                     Writes the actual input
1008                 '''
1009                 myFormats = [
1010                     ('Input files','*.inp'),
1011                         ('All files','*.*')
1012                 ]
1013                 # Write error handling for empty sequence
1014                 #
1015                 s=self.gr3.t1.getvalue()
1016                 if len(s.strip())==0:
1017                         tkMessageBox.showerror("NEED SEQUENCE DATA!", "NEED SEQUENCE DATA!\n\nYou have not loaded the sequence information. Please click \"Refresh\", choose an object from the list and click \"Get sequence\".")
1018                 else:
1019                         # Display dialog window
1020                         fout = tkFileDialog.asksaveasfile(parent=self,mode='w',filetypes=myFormats,title='Save input')
1021                         if fout:
1022                                 print "Saving input file %s" % fout.name
1023                                 # Get input header
1024                                 text2save=self.fortran_format(self.e1.get())
1025                                 # Get main options
1026                                 mainopt="SEED="+self.gr1.e1.get()+" "
1027                                 if self.OM1Val.get()=="MD":
1028                                         mainopt+="MD PDBREF"
1029                                         if self.gr1.md.om1.getvalue()=="PDB":
1030                                                 mainopt+=" PDBSTART"
1031                                         elif self.gr1.md.om1.getvalue()=="extended":
1032                                                 mainopt+=" EXTCONF"
1033                                         else:
1034                                                 mainopt+=" RAND_CONF"
1035                                 elif self.OM1Val.get()=="REMD/MREMD":
1036                                         mainopt+="RE PDBREF"
1037                                         if self.gr1.md.om1.getvalue()=="PDB":
1038                                                 mainopt+=" PDBSTART"
1039                                         elif self.gr1.md.om1.getvalue()=="extended":
1040                                                 mainopt+=" EXTCONF"
1041                                         else:
1042                                                 mainopt+=" RAND_CONF"
1043
1044                                 elif self.OM1Val.get()=="MINIMIZE":
1045                                         mainopt+="PDBREF PDBSTART MINIMIZE RESCALE_MODE=0"
1046                                         if self.CART.get():
1047                                                 mainopt+=" CART"
1048                                         if self.OVERLAP.get():
1049                                                 mainopt+=" OVERLAP"
1050                                         if self.NOSEARCHSC.get():
1051                                                 mainopt+=" NOSERARCHSC"
1052                                 text2save+=self.fortran_format(mainopt)
1053                                 # Get aux options
1054
1055                                 if self.OM1Val.get()=="MD":
1056                                         text2save+=self.fortran_format(self.get_md_opt())
1057                                 elif self.OM1Val.get()=="REMD/MREMD":
1058                                         text2save+=self.fortran_format(self.get_md_opt())
1059                                         text2save+=self.fortran_format(self.get_mremd_opt())
1060                                         text2save+=self.fortran_format(self.get_mremd_temp_opt())
1061                                         text2save+=self.fortran_format(self.get_mremd_replicas())
1062                                 elif self.OM1Val.get()=="MINIMIZE":
1063                                         text2save+=self.fortran_format(self.get_minim_opt())
1064
1065                                 # Get force fields parameters
1066                                 text2save+=self.fortran_format(self.get_weights())
1067
1068                                 # PDB reference
1069                                 pdbreffn=str(self.cb2.getvalue()[0])+"_pdbref.pdb"
1070                                 text2save+=pdbreffn+"\n"
1071                                 print "Saving PDB reference structure %s" % (os.path.join(os.path.dirname(fout.name),pdbreffn))
1072                                 cmd.save(os.path.join(os.path.dirname(fout.name),pdbreffn), self.cb2.getvalue()[0])
1073
1074                                 # C-shell script
1075                                 cshellfn=os.path.join(os.path.dirname(fout.name),"unres_"+os.path.basename(os.path.splitext(fout.name)[0])+".csh")
1076                                 print "Writing C-shell script %s" % (cshellfn)
1077                                 prefix=os.path.basename(os.path.splitext(fout.name)[0])
1078                                 self.write_cshell(cshellfn,prefix)
1079
1080                                 # Get sequence data
1081                                 text2save+=self.get_seq_data()
1082
1083                                 fout.write(text2save)
1084                                 fout.close()
1085
1086                                 # ENV Varaiables info
1087                                 self.setenv_info()